getftype uses the read names to determine the file type ( 0 == fastq, 1 == fasta and 2 == sam). In practice read names should be considered free text and I think you should prabably get the file type from the extension or ask the user as a parameter. In our case since we do not use this read naming scheme it was detecting our input as fasta even though it was fastq and this lead to interger overruns.
getftype uses the read names to determine the file type ( 0 == fastq, 1 == fasta and 2 == sam). In practice read names should be considered free text and I think you should prabably get the file type from the extension or ask the user as a parameter. In our case since we do not use this read naming scheme it was detecting our input as fasta even though it was fastq and this lead to interger overruns.